[gmx-users] Forces are large - How to track down the culprit

[Shay Amram]

< Is this reproducible?
Yes. I've taken the same simulation and had it re-run and got the same error
at the exact same frame (frame 693, which is timeframe 6930).

<You could try to fork off a tpr file using tpbconv -f -e -s -o just 
<before this happens and rerun it.
I did something similar to what you suggest before posting here:
Oddly enough the Warning did not occur: I ran the simulation up to 6000ps
and then continued the simulation to another 4000ps and the simulation ran
correctly and without any problems.

< It can also be combined by input parameters, e.g. too large time step, 
<too infrequent neighborsearching etc., use of cutoffs.
If no other suggestions I'll try working that angle too, since a lot of my
simulations are running with very similar mdp parameters without problems.

Thanks again for your prompt reply,
-Shay



Shay Amram wrote:
> Of course. I'm using version 3.3.3 of GROMACS. 
> -Shay
> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Mark Abraham
> Sent: Tuesday, December 30, 2008 02:59 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Forces are large - How to track down the culprit
> 
> Shay Amram wrote:
>> Greetings dear Gromacs users,
>>
>>  
>>
>> I have recently been simulating a POPG membrane* in water (SPC). Several 
>> of my simulations after running well into the 10ns and 20ns are 
>> sometimes getting a "Forces for atom X are large".  
>>
>> I'm rather unsure as to the cause of this situation. Moreover, as far as 
>> I can tell from viewing the simulation, the system _does NOT_ explode 
>> (as may be suggested by wiki.gromacs and some previous answers to this 
>> kind of situation). The rest of the simulation looks much as it did in 
>> the beginning.
>>
>> I would be interested (and thankful!) to hear any of your opinions as to 
>> why I'm getting this message (or how to catch the culprit), and more 
>> importantly, how to prevent it from happening in the future.
> 
> During this version-transitive period, it's always right to report the 
> GROMACS version that you're using. It would normally be right to be 
> using the most recent version (4.0.2) if encountering problems.
> 
> Mark
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